Description Usage Arguments Details Value Examples
This function takes the output of slingshot
(or
getCurves
) and attempts to embed the curves in a different
coordinate space than the one in which they were constructed. This should
be considered as a visualization tool, only.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37  embedCurves(x, newDimRed, ...)
## S4 method for signature 'SlingshotDataSet,matrix'
embedCurves(
x,
newDimRed,
shrink = NULL,
stretch = NULL,
approx_points = NULL,
smoother = NULL,
shrink.method = NULL,
...
)
## S4 method for signature 'SingleCellExperiment,matrix'
embedCurves(
x,
newDimRed,
shrink = NULL,
stretch = NULL,
approx_points = NULL,
smoother = NULL,
shrink.method = NULL,
...
)
## S4 method for signature 'SingleCellExperiment,character'
embedCurves(
x,
newDimRed,
shrink = NULL,
stretch = NULL,
approx_points = NULL,
smoother = NULL,
shrink.method = NULL,
...
)

x 
an object containing 
newDimRed 
a matrix representing the new coordinate space in which to
embed the 
... 
Additional parameters to pass to scatter plot smoothing function,

shrink 
logical or numeric between 0 and 1, determines whether and how much to shrink branching lineages toward their average prior to the split. 
stretch 
numeric factor by which curves can be extrapolated beyond
endpoints. Default is 
approx_points 
numeric, whether curves should be approximated by a
fixed number of points. If 
smoother, 
choice of scatter plot smoother. Same as

shrink.method 
character denoting how to determine the appropriate
amount of shrinkage for a branching lineage. Accepted values are the same
as for 
Many of the same parameters are used here as in getCurves
.
This function attempts to translate curves from one reduced dimensional
space to another by predicting each dimension as a function of pseudotime
(ie. the new curve is determined by a series of scatterplot smoothers
predicting the coordinates in the new space as a function of pseudotime).
Because the pseudotime values are not changed, this amounts to a single
iteration of the iterative curvefitting process used by getCurves
.
Note that nonlinear dimensionality reduction techniques (such as tSNE and UMAP) may produce discontinuities not observed in other spaces. Use caution when embedding curves in these spaces.
a SlingshotDataSet
containing curves in the new space.
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